Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009445.1 Corchorus capsularis cultivar CVL-1 contig09466, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 28792
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33


Found at i:339 original size:2 final size:2

Alignment explanation


    Indices: 332--366  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

        322 CTATTTTGAT

                                                                
        332 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

        367 GTTAGATCCT


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:1358 original size:39 final size:39

Alignment explanation


    Indices: 1315--1393  Score: 140
    Period size: 39  Copynumber: 2.0  Consensus size: 39

       1305 ATTTCAATCT

                       *                           
       1315 AAGTGACTCAATTTTGGATTAATAGATTACCGAATATGA
          1 AAGTGACTCAACTTTGGATTAATAGATTACCGAATATGA

                    *                              
       1354 AAGTGACTTAACTTTGGATTAATAGATTACCGAATATGA
          1 AAGTGACTCAACTTTGGATTAATAGATTACCGAATATGA

             
       1393 A
          1 A

       1394 GTTTAAGGGG


Statistics
Matches: 38,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  39   38  1.00

ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33


Consensus pattern (39 bp):   
AAGTGACTCAACTTTGGATTAATAGATTACCGAATATGA

Found at i:3486 original size:21 final size:22

Alignment explanation


    Indices: 3427--3486  Score: 65
    Period size: 21  Copynumber: 2.9  Consensus size: 22

       3417 TATTGTTTAG

                      *           
       3427 GTACTGTACATATGAGATTACA
          1 GTACTGTACAGATGAGATTACA

                         * *      
       3449 --A-TGTACAGATTAAATTA-A
          1 GTACTGTACAGATGAGATTACA

                                
       3467 GTACTGTACAGATGAGATTA
          1 GTACTGTACAGATGAGATTA

       3487 TTAGAACATT


Statistics
Matches: 30,  Mismatches: 5, Indels: 7
        0.71            0.12        0.17

Matches are distributed among these distances:
  18    1  0.03
  19   13  0.43
  20    2  0.07
  21   14  0.47

ACGTcount: A:0.40, C:0.10, G:0.18, T:0.32


Consensus pattern (22 bp):   
GTACTGTACAGATGAGATTACA

Found at i:6960 original size:2 final size:2

Alignment explanation


    Indices: 6953--6978  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       6943 ATAAGTACAA

                                                  
       6953 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

       6979 GAAAGTTTCT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:16143 original size:29 final size:31

Alignment explanation


    Indices: 16072--16146  Score: 82
    Period size: 29  Copynumber: 2.5  Consensus size: 31

      16062 TAAATAGCCC

                       *                    
      16072 CTTTGCCCCCTAAACTTTGCAAATTTAGGCCA
          1 CTTTGCCCCCTGAACTTT-CAAATTTAGGCCA

            **   *                    *    
      16104 GATTGTCCCCTGAACTTT-AAA-TTATGCCA
          1 CTTTGCCCCCTGAACTTTCAAATTTAGGCCA

                          
      16133 CTTTGCCCCCTGAA
          1 CTTTGCCCCCTGAA

      16147 TTTGTAAAAT


Statistics
Matches: 35,  Mismatches: 8, Indels: 3
        0.76            0.17        0.07

Matches are distributed among these distances:
  29   18  0.51
  30    3  0.09
  32   14  0.40

ACGTcount: A:0.24, C:0.31, G:0.13, T:0.32


Consensus pattern (31 bp):   
CTTTGCCCCCTGAACTTTCAAATTTAGGCCA

Found at i:21023 original size:17 final size:17

Alignment explanation


    Indices: 21001--21033  Score: 57
    Period size: 17  Copynumber: 1.9  Consensus size: 17

      20991 TCCCATGGTC

                             
      21001 CGGGTCACGCGCGATCG
          1 CGGGTCACGCGCGATCG

                  *         
      21018 CGGGTCGCGCGCGATC
          1 CGGGTCACGCGCGATC

      21034 CGGACCATGG


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.09, C:0.36, G:0.42, T:0.12


Consensus pattern (17 bp):   
CGGGTCACGCGCGATCG
Done.